megadetector 5.0.11__py3-none-any.whl → 5.0.13__py3-none-any.whl

megadetector/utils/md_tests.py

@@ -0,0 +1,1164 @@
+"""
+
+md_tests.py
+
+A series of tests to validate basic repo functionality and verify either "correct"
+inference behavior, or - when operating in environments other than the training
+environment - acceptable deviation from the correct results.
+
+This module should not depend on anything else in this repo outside of the 
+tests themselves, even if it means some duplicated code (e.g. for downloading files),
+since much of what it tries to test is, e.g., imports.
+
+"""
+
+#%% Imports and constants
+
+### Only standard imports belong here, not MD-specific imports ###
+
+import os
+import json
+import glob
+import tempfile
+import urllib
+import urllib.request
+import zipfile
+import subprocess
+import argparse
+import inspect
+
+
+#%% Classes
+
+class MDTestOptions:
+    """
+    Options controlling test behavior
+    """
+    
+    def __init__(self):
+    
+        ## Required ##
+    
+        #: Force CPU execution
+        self.disable_gpu = False
+        
+        #: If GPU execution is requested, but a GPU is not available, should we error?
+        self.cpu_execution_is_error = False
+        
+        #: Skip tests related to video processing
+        self.skip_video_tests = False
+        
+        #: Skip tests launched via Python functions (as opposed to CLIs)
+        self.skip_python_tests = False
+        
+        #: Skip CLI tests
+        self.skip_cli_tests = False
+        
+        #: Force a specific folder for temporary input/output
+        self.scratch_dir = None
+        
+        #: Where does the test data live?
+        self.test_data_url = 'https://lila.science/public/md-test-package.zip'
+        
+        #: Download test data even if it appears to have already been downloaded
+        self.force_data_download = False
+        
+        #: Unzip test data even if it appears to have already been unzipped
+        self.force_data_unzip = False
+        
+        #: By default, any unexpected behavior is an error; this forces most errors to
+        #: be treated as warnings.
+        self.warning_mode = False
+        
+        #: How much deviation from the expected detection coordinates should we allow before
+        #: a disrepancy becomes an error?
+        self.max_coord_error = 0.001
+        
+        #: How much deviation from the expected confidence values should we allow before
+        #: a disrepancy becomes an error?    
+        self.max_conf_error = 0.005
+        
+        #: Current working directory when running CLI tests
+        self.cli_working_dir = None
+        
+        #: YOLOv5 installation, only relevant if we're testing run_inference_with_yolov5_val. 
+        #:
+        #: If this is None, we'll skip that test.
+        self.yolo_working_dir = None
+        
+        #: fourcc code to use for video tests that involve rendering video
+        self.video_fourcc = 'mp4v'   
+        
+        #: Default model to use for testing (filename, URL, or well-known model string)
+        self.default_model = 'MDV5A'
+
+        #: For comparison tests, use a model that produces slightly different output        
+        self.alt_model = 'MDV5B'
+        
+        #: PYTHONPATH to set for CLI tests; if None, inherits from the parent process.  Only
+        #: impacts the called functions, not the parent process.
+        self.cli_test_pythonpath = None
+
+# ...class MDTestOptions()
+
+
+#%% Support functions
+
+def get_expected_results_filename(gpu_is_available):
+    """
+    Expected results vary just a little across inference environments, particularly
+    between PT 1.x and 2.x, so when making sure things are working acceptably, we 
+    compare to a reference file that matches the current environment.
+    
+    This function gets the correct filename to compare to current results, depending
+    on whether a GPU is available.
+    
+    Args:
+        gpu_is_available (bool): whether a GPU is available
+        
+    Returns:
+        str: relative filename of the results file we should use (within the test
+        data zipfile)
+    """
+    
+    if gpu_is_available:
+        hw_string = 'gpu'
+    else:
+        hw_string = 'cpu'
+    import torch
+    torch_version = str(torch.__version__)
+    if torch_version.startswith('1'):
+        assert torch_version == '1.10.1', 'Only tested against PT 1.10.1 and PT 2.x'
+        pt_string = 'pt1.10.1'
+    else:
+        assert torch_version.startswith('2'), 'Unknown torch version: {}'.format(torch_version)
+        pt_string = 'pt2.x'
+    
+    # A hack for now to account for the fact that even with acceleration enabled and PT2 
+    # installed, Apple silicon appears to provide the same results as CPU/PT1 inference
+    try:
+        import torch
+        m1_inference = torch.backends.mps.is_built and torch.backends.mps.is_available()
+        if m1_inference:
+            print('I appear to be running on M1/M2 hardware')
+            hw_string = 'cpu'
+            pt_string = 'pt1.10.1'
+    except Exception:
+        pass
+    
+    return 'md-test-results-{}-{}.json'.format(hw_string,pt_string)
+    
+    
+def download_test_data(options=None):
+    """
+    Downloads the test zipfile if necessary, unzips if necessary.
+    
+    Args:
+        options (MDTestOptions, optional): see MDTestOptions for details
+        
+    Returns:
+        MDTestOptions: the same object passed in as input, or the options that
+        were used if [options] was supplied as None
+    """
+
+    if options is None:
+        options = MDTestOptions()
+        
+    if options.scratch_dir is None:        
+        tempdir_base = tempfile.gettempdir()
+        scratch_dir = os.path.join(tempdir_base,'md-tests')
+    else:
+        scratch_dir = options.scratch_dir
+    
+    os.makedirs(scratch_dir,exist_ok=True)    
+    
+    # See whether we've already downloaded the data zipfile
+    download_zipfile = True        
+    if not options.force_data_download:
+        local_zipfile = os.path.join(scratch_dir,options.test_data_url.split('/')[-1])
+        if os.path.isfile(local_zipfile):
+            url_info = urllib.request.urlopen(options.test_data_url).info()
+            remote_size = int(url_info['Content-Length'])
+            target_file_size = os.path.getsize(local_zipfile)
+            if remote_size == target_file_size:
+                download_zipfile = False
+    
+    if download_zipfile:
+        print('Downloading test data zipfile')
+        urllib.request.urlretrieve(options.test_data_url, local_zipfile)
+        print('Finished download to {}'.format(local_zipfile))
+    else:
+        print('Bypassing test data zipfile download for {}'.format(local_zipfile))
+    
+    
+    ## Unzip data
+    
+    zipf = zipfile.ZipFile(local_zipfile)    
+    zip_contents = zipf.filelist
+    
+    # file_info = zip_contents[1]
+    for file_info in zip_contents:
+        
+        expected_size = file_info.file_size
+        if expected_size == 0:
+            continue
+        fn_relative = file_info.filename
+        target_file = os.path.join(scratch_dir,fn_relative)
+        unzip_file = True
+        if (not options.force_data_unzip) and os.path.isfile(target_file):
+            existing_file_size = os.path.getsize(target_file)
+            if existing_file_size == expected_size:
+                unzip_file = False
+        if unzip_file:
+            os.makedirs(os.path.dirname(target_file),exist_ok=True)
+            with open(target_file,'wb') as f:
+                f.write(zipf.read(fn_relative))
+            
+    # ...for each file in the zipfile
+    
+    # Warn if file are present that aren't expected
+    test_files = glob.glob(os.path.join(scratch_dir,'**/*'), recursive=True)
+    test_files = [os.path.relpath(fn,scratch_dir).replace('\\','/') for fn in test_files]
+    test_files_set = set(test_files)
+    expected_images_set = set(zipf.namelist())
+    for fn in expected_images_set:
+        if fn.endswith('/'):
+            continue
+        assert fn in test_files_set, 'File {} is missing from the test image folder'.format(fn)
+    
+    # Populate the test options with test data information
+    options.scratch_dir = scratch_dir
+    options.all_test_files = test_files
+    options.test_images = [fn for fn in test_files if os.path.splitext(fn.lower())[1] in ('.jpg','.jpeg','.png')]
+    options.test_videos = [fn for fn in test_files if os.path.splitext(fn.lower())[1] in ('.mp4','.avi')]    
+    options.test_videos = [fn for fn in options.test_videos if 'rendered' not in fn]
+    options.test_videos = [fn for fn in options.test_videos if \
+                           os.path.isfile(os.path.join(scratch_dir,fn))]
+        
+    print('Finished unzipping and enumerating test data')
+    
+    return options
+
+# ...def download_test_data(...)
+
+
+def is_gpu_available(verbose=True):
+    """
+    Checks whether a GPU (including M1/M2 MPS) is available.
+    
+    Args:
+        verbose (bool, optional): enable additional debug console output
+    
+    Returns:
+        bool: whether a GPU is available
+    """
+    
+    # Import torch inside this function, so we have a chance to set CUDA_VISIBLE_DEVICES
+    # before checking GPU availability.
+    import torch
+    gpu_available = torch.cuda.is_available()
+    
+    if gpu_available:
+        if verbose:
+            print('CUDA available: {}'.format(gpu_available))
+            device_ids = list(range(torch.cuda.device_count()))
+            if len(device_ids) > 1:
+                print('Found multiple devices: {}'.format(str(device_ids)))
+    else:
+        try:
+            gpu_available = torch.backends.mps.is_built and torch.backends.mps.is_available()
+        except AttributeError:
+            pass
+        if gpu_available:
+            print('Metal performance shaders available')
+    
+    if not gpu_available:
+        print('No GPU available')
+        
+    return gpu_available            
+
+# ...def is_gpu_available(...)     
+
+
+def output_files_are_identical(fn1,fn2,verbose=False):
+    """
+    Checks whether two MD-formatted output files are identical other than file sorting.
+    
+    Args:
+        fn1 (str): the first filename to compare
+        fn2 (str): the second filename to compare
+    
+    Returns:
+        bool: whether [fn1] and [fn2] are identical other than file sorting.
+    """
+    
+    if verbose:
+        print('Comparing {} to {}'.format(fn1,fn2))
+    
+    with open(fn1,'r') as f:
+         fn1_results = json.load(f)
+    fn1_results['images'] = \
+         sorted(fn1_results['images'], key=lambda d: d['file'])
+    
+    with open(fn2,'r') as f:
+         fn2_results = json.load(f)
+    fn2_results['images'] = \
+         sorted(fn2_results['images'], key=lambda d: d['file'])
+     
+    if len(fn1_results['images']) != len(fn1_results['images']):
+        if verbose:
+            print('{} images in {}, {} images in {}'.format(
+                len(fn1_results['images']),fn1,
+                len(fn2_results['images']),fn2))
+        return False
+    
+    for i_image,fn1_image in enumerate(fn1_results['images']):
+        
+        fn2_image = fn2_results['images'][i_image]
+        
+        if fn1_image['file'] != fn2_image['file']:
+            if verbose:
+                print('Filename difference: {} vs {} '.format(fn1_image['file'],fn1_image['file']))
+            return False
+            
+        if fn1_image != fn2_image:
+            if verbose:
+                print('Image-level difference in image {}'.format(fn1_image['file']))
+            return False
+        
+    return True
+
+# ...def output_files_are_identical(...)
+   
+
+def _args_to_object(args, obj):
+    """
+    Copies all fields from a Namespace (typically the output from parse_args) to an
+    object. Skips fields starting with _. Does not check existence in the target
+    object.
+
+    Args:
+        args (argparse.Namespace): the namespace to convert to an object
+        obj (object): object whose whose attributes will be updated
+        
+    Returns:
+        object: the modified object (modified in place, but also returned)
+    """
+    
+    for n, v in inspect.getmembers(args):
+        if not n.startswith('_'):
+            setattr(obj, n, v)
+
+    return obj
+
+    
+#%% CLI functions
+
+# These are copied from process_utils.py to avoid imports outside of the test
+# functions.
+
+os.environ["PYTHONUNBUFFERED"] = "1"
+
+def execute(cmd):
+    """
+    Runs [cmd] (a single string) in a shell, yielding each line of output to the caller.
+    
+    Args:
+        cmd (str): command to run
+    
+    Returns:
+        int: the command's return code, always zero, otherwise a CalledProcessError is raised
+    """
+ 
+    # https://stackoverflow.com/questions/4417546/constantly-print-subprocess-output-while-process-is-running
+    popen = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT,
+                             shell=True, universal_newlines=True)
+    for stdout_line in iter(popen.stdout.readline, ""):
+        yield stdout_line
+    popen.stdout.close()
+    return_code = popen.wait()
+    if return_code:
+        raise subprocess.CalledProcessError(return_code, cmd)
+    return return_code
+
+
+def execute_and_print(cmd,print_output=True,catch_exceptions=False):
+    """
+    Runs [cmd] (a single string) in a shell, capturing (and optionally printing) output.
+    
+    Args:
+        cmd (str): command to run
+        print_output (bool, optional): whether to print output from [cmd]
+    
+    Returns:
+        dict: a dictionary with fields "status" (the process return code) and "output"
+        (the content of stdout)
+    """
+
+    to_return = {'status':'unknown','output':''}
+    output=[]
+    try:
+        for s in execute(cmd):
+            output.append(s)
+            if print_output:
+                print(s,end='',flush=True)
+        to_return['status'] = 0
+    except subprocess.CalledProcessError as cpe:
+        if not catch_exceptions:
+            raise
+        print('execute_and_print caught error: {}'.format(cpe.output))
+        to_return['status'] = cpe.returncode
+    to_return['output'] = output
+   
+    return to_return
+
+
+#%% Python tests
+
+def run_python_tests(options):
+    """
+    Runs Python-based (as opposed to CLI-based) package tests.
+    
+    Args:
+        options (MDTestOptions): see MDTestOptions for details
+    """
+    
+    print('\n*** Starting module tests ***\n')
+    
+    ## Prepare data
+    
+    download_test_data(options)
+    
+    
+    ## Run inference on an image
+    
+    from megadetector.detection import run_detector
+    from megadetector.visualization import visualization_utils as vis_utils
+    image_fn = os.path.join(options.scratch_dir,options.test_images[0])
+    model = run_detector.load_detector(options.default_model)
+    pil_im = vis_utils.load_image(image_fn)
+    result = model.generate_detections_one_image(pil_im) # noqa
+
+    
+    ## Run inference on a folder
+    
+    from megadetector.detection.run_detector_batch import load_and_run_detector_batch,write_results_to_file
+    from megadetector.utils import path_utils
+
+    image_folder = os.path.join(options.scratch_dir,'md-test-images')
+    assert os.path.isdir(image_folder), 'Test image folder {} is not available'.format(image_folder)
+    inference_output_file = os.path.join(options.scratch_dir,'folder_inference_output.json')
+    image_file_names = path_utils.find_images(image_folder,recursive=True)
+    results = load_and_run_detector_batch(options.default_model, image_file_names, quiet=True)
+    _ = write_results_to_file(results,inference_output_file,
+                              relative_path_base=image_folder,detector_file=options.default_model)
+
+    # Read results
+    with open(inference_output_file,'r') as f:
+        results_from_file = json.load(f) # noqa
+    
+
+    ## Verify results
+
+    # Read expected results
+    expected_results_filename = get_expected_results_filename(is_gpu_available(verbose=False))
+    
+    with open(os.path.join(options.scratch_dir,expected_results_filename),'r') as f:
+        expected_results = json.load(f)
+            
+    filename_to_results = {im['file'].replace('\\','/'):im for im in results_from_file['images']}
+    filename_to_results_expected = {im['file'].replace('\\','/'):im for im in expected_results['images']}
+    
+    assert len(filename_to_results) == len(filename_to_results_expected), \
+        'Error: expected {} files in results, found {}'.format(
+            len(filename_to_results_expected),
+            len(filename_to_results))
+    
+    max_coord_error = 0
+    max_conf_error = 0
+    
+    # fn = next(iter(filename_to_results.keys()))
+    for fn in filename_to_results.keys():
+                
+        actual_image_results = filename_to_results[fn]
+        expected_image_results = filename_to_results_expected[fn]
+        
+        if 'failure' in actual_image_results:
+            assert 'failure' in expected_image_results and \
+                'detections' not in actual_image_results and \
+                'detections' not in expected_image_results
+            continue
+        assert 'failure' not in expected_image_results
+        
+        actual_detections = actual_image_results['detections']
+        expected_detections = expected_image_results['detections']
+        
+        s = 'expected {} detections for file {}, found {}'.format(
+            len(expected_detections),fn,len(actual_detections))
+        s += '\nExpected results file: {}\nActual results file: {}'.format(
+            expected_results_filename,inference_output_file)
+        
+        if options.warning_mode:
+            if len(actual_detections) != len(expected_detections):
+                print('Warning: {}'.format(s))
+            continue
+        assert len(actual_detections) == len(expected_detections), \
+            'Error: {}'.format(s)
+        
+        # i_det = 0
+        for i_det in range(0,len(actual_detections)):
+            actual_det = actual_detections[i_det]
+            expected_det = expected_detections[i_det]
+            assert actual_det['category'] == expected_det['category']
+            conf_err = abs(actual_det['conf'] - expected_det['conf'])
+            coord_differences = []
+            for i_coord in range(0,4):
+                coord_differences.append(abs(actual_det['bbox'][i_coord]-expected_det['bbox'][i_coord]))
+            coord_err = max(coord_differences)
+            
+            if conf_err > max_conf_error:
+                max_conf_error = conf_err
+            if coord_err > max_coord_error:
+                max_coord_error = coord_err
+        
+        # ...for each detection
+        
+    # ...for each image
+    
+    if not options.warning_mode:
+        
+        assert max_conf_error <= options.max_conf_error, \
+            'Confidence error {} is greater than allowable ({})'.format(
+                max_conf_error,options.max_conf_error)
+        
+        assert max_coord_error <= options.max_coord_error, \
+            'Coord error {} is greater than allowable ({})'.format(
+                max_coord_error,options.max_coord_error)
+        
+    print('Max conf error: {}'.format(max_conf_error))
+    print('Max coord error: {}'.format(max_coord_error))
+
+
+    ## Postprocess results
+    
+    from megadetector.postprocessing.postprocess_batch_results import \
+        PostProcessingOptions,process_batch_results
+    postprocessing_options = PostProcessingOptions()
+    
+    postprocessing_options.md_results_file = inference_output_file
+    postprocessing_options.output_dir = os.path.join(options.scratch_dir,'postprocessing_output')
+    postprocessing_options.image_base_dir = image_folder
+    
+    postprocessing_results = process_batch_results(postprocessing_options)
+    assert os.path.isfile(postprocessing_results.output_html_file), \
+        'Postprocessing output file {} not found'.format(postprocessing_results.output_html_file)
+    
+        
+    ## Partial RDE test
+    
+    from megadetector.postprocessing.repeat_detection_elimination.repeat_detections_core import \
+        RepeatDetectionOptions, find_repeat_detections
+    
+    rde_options = RepeatDetectionOptions()
+    rde_options.occurrenceThreshold = 2
+    rde_options.confidenceMin = 0.001
+    rde_options.outputBase = os.path.join(options.scratch_dir,'rde_working_dir')
+    rde_options.imageBase = image_folder
+    rde_output_file = inference_output_file.replace('.json','_filtered.json')
+    assert rde_output_file != inference_output_file
+    rde_results = find_repeat_detections(inference_output_file, rde_output_file, rde_options)
+    assert os.path.isfile(rde_results.filterFile),\
+        'Could not find RDE output file {}'.format(rde_results.filterFile)
+        
+    
+    ## Run inference on a folder (with YOLOv5 val script)
+    
+    if options.yolo_working_dir is None:
+        
+        print('Skipping YOLO val inference tests, no YOLO folder supplied')
+        
+    else:
+            
+        from megadetector.detection.run_inference_with_yolov5_val import \
+            YoloInferenceOptions, run_inference_with_yolo_val
+        
+        inference_output_file_yolo_val = os.path.join(options.scratch_dir,'folder_inference_output_yolo_val.json')
+        
+        yolo_inference_options = YoloInferenceOptions()
+        yolo_inference_options.input_folder = os.path.join(options.scratch_dir,'md-test-images')
+        yolo_inference_options.output_file = inference_output_file_yolo_val
+        yolo_inference_options.yolo_working_folder = options.yolo_working_dir
+        yolo_inference_options.model_filename = options.default_model
+        yolo_inference_options.augment = False
+        yolo_inference_options.overwrite_handling = 'overwrite'
+        
+        run_inference_with_yolo_val(yolo_inference_options)
+        
+        # Run again, without symlinks this time
+        
+        from megadetector.utils.path_utils import insert_before_extension
+        inference_output_file_yolo_val_no_links = insert_before_extension(inference_output_file_yolo_val,
+                                                                          'no-links')
+        yolo_inference_options.output_file = inference_output_file_yolo_val_no_links
+        yolo_inference_options.use_symlinks = False
+        run_inference_with_yolo_val(yolo_inference_options)
+    
+        # Run again, with chunked inference and symlinks
+        
+        inference_output_file_yolo_val_checkpoints = insert_before_extension(inference_output_file_yolo_val,
+                                                                          'checkpoints')
+        yolo_inference_options.output_file = inference_output_file_yolo_val_checkpoints
+        yolo_inference_options.use_symlinks = True
+        yolo_inference_options.checkpoint_frequency = 5
+        run_inference_with_yolo_val(yolo_inference_options)
+        
+        # Run again, with chunked inference and no symlinks
+        
+        inference_output_file_yolo_val_checkpoints_no_links = \
+            insert_before_extension(inference_output_file_yolo_val,'checkpoints-no-links')
+        yolo_inference_options.output_file = inference_output_file_yolo_val_checkpoints_no_links
+        yolo_inference_options.use_symlinks = False
+        yolo_inference_options.checkpoint_frequency = 5
+        run_inference_with_yolo_val(yolo_inference_options)
+    
+        fn1 = inference_output_file_yolo_val
+        
+        output_files_to_compare = [
+            inference_output_file_yolo_val_no_links,
+            inference_output_file_yolo_val_checkpoints,
+            inference_output_file_yolo_val_checkpoints_no_links
+            ]
+    
+        for fn2 in output_files_to_compare:
+            assert output_files_are_identical(fn1, fn2, verbose=True)
+                            
+    # ...if we need to run the YOLO val inference tests
+    
+    
+    if not options.skip_video_tests:
+        
+        ## Video test (single video)
+       
+        from megadetector.detection.process_video import ProcessVideoOptions, process_video
+        
+        video_options = ProcessVideoOptions()
+        video_options.model_file = options.default_model
+        video_options.input_video_file = os.path.join(options.scratch_dir,options.test_videos[0])
+        video_options.output_json_file = os.path.join(options.scratch_dir,'single_video_output.json')
+        video_options.output_video_file = os.path.join(options.scratch_dir,'video_scratch/rendered_video.mp4')
+        video_options.frame_folder = os.path.join(options.scratch_dir,'video_scratch/frame_folder')
+        video_options.frame_rendering_folder = os.path.join(options.scratch_dir,'video_scratch/rendered_frame_folder')    
+        video_options.render_output_video = True
+        # video_options.keep_rendered_frames = False
+        # video_options.keep_rendered_frames = False
+        video_options.force_extracted_frame_folder_deletion = True
+        video_options.force_rendered_frame_folder_deletion = True
+        # video_options.reuse_results_if_available = False
+        # video_options.reuse_frames_if_available = False
+        video_options.recursive = True
+        video_options.verbose = False
+        video_options.fourcc = options.video_fourcc
+        # video_options.rendering_confidence_threshold = None
+        # video_options.json_confidence_threshold = 0.005
+        video_options.frame_sample = 5    
+        video_options.n_cores = 5
+        # video_options.debug_max_frames = -1
+        # video_options.class_mapping_filename = None
+        
+        _ = process_video(video_options)
+    
+        assert os.path.isfile(video_options.output_video_file), \
+            'Python video test failed to render output video file'
+        assert os.path.isfile(video_options.output_json_file), \
+            'Python video test failed to render output .json file'
+            
+        
+        ## Video test (folder)
+        
+        from megadetector.detection.process_video import ProcessVideoOptions, process_video_folder
+        
+        video_options = ProcessVideoOptions()
+        video_options.model_file = options.default_model
+        video_options.input_video_file = os.path.join(options.scratch_dir,
+                                                      os.path.dirname(options.test_videos[0]))
+        video_options.output_json_file = os.path.join(options.scratch_dir,'video_folder_output.json')
+        # video_options.output_video_file = None
+        video_options.frame_folder = os.path.join(options.scratch_dir,'video_scratch/frame_folder')
+        video_options.frame_rendering_folder = os.path.join(options.scratch_dir,'video_scratch/rendered_frame_folder')    
+        video_options.render_output_video = False
+        # video_options.keep_rendered_frames = False
+        # video_options.keep_rendered_frames = False
+        video_options.force_extracted_frame_folder_deletion = True
+        video_options.force_rendered_frame_folder_deletion = True
+        # video_options.reuse_results_if_available = False
+        # video_options.reuse_frames_if_available = False
+        video_options.recursive = True
+        video_options.verbose = True
+        video_options.fourcc = options.video_fourcc
+        # video_options.rendering_confidence_threshold = None
+        # video_options.json_confidence_threshold = 0.005
+        video_options.frame_sample = 5    
+        video_options.n_cores = 5
+        # video_options.debug_max_frames = -1
+        # video_options.class_mapping_filename = None
+        
+        _ = process_video_folder(video_options)
+    
+        assert os.path.isfile(video_options.output_json_file), \
+            'Python video test failed to render output .json file'
+        
+    # ...if we're not skipping video tests
+    
+    print('\n*** Finished module tests ***\n')
+
+# ...def run_python_tests(...)
+
+
+#%% Command-line tests
+
+def run_cli_tests(options):
+    """
+    Runs CLI (as opposed to Python-based) package tests.
+    
+    Args:
+        options (MDTestOptions): see MDTestOptions for details
+    """
+    
+    print('\n*** Starting CLI tests ***\n')
+    
+    
+    ## Environment management
+    
+    if options.cli_test_pythonpath is not None:
+        os.environ['PYTHONPATH'] = options.cli_test_pythonpath 
+        
+        
+    ## chdir if necessary
+    
+    if options.cli_working_dir is not None:
+        os.chdir(options.cli_working_dir)
+    
+    
+    ## Prepare data
+    
+    download_test_data(options)
+    
+    
+    ## Run inference on an image
+    
+    image_fn = os.path.join(options.scratch_dir,options.test_images[0])
+    output_dir = os.path.join(options.scratch_dir,'single_image_test')
+    if options.cli_working_dir is None:
+        cmd = 'python -m megadetector.detection.run_detector'
+    else:
+        cmd = 'python megadetector/detection/run_detector.py'
+    cmd += ' "{}" --image_file "{}" --output_dir "{}"'.format(
+        options.default_model,image_fn,output_dir)
+    print('Running: {}'.format(cmd))
+    cmd_results = execute_and_print(cmd)
+    
+    if options.cpu_execution_is_error:
+        gpu_available_via_cli = False
+        for s in cmd_results['output']:
+            if 'GPU available: True' in s:
+                gpu_available_via_cli = True
+                break
+        if not gpu_available_via_cli:
+            raise Exception('GPU execution is required, but not available')
+
+    
+    ## Run inference on a folder
+    
+    image_folder = os.path.join(options.scratch_dir,'md-test-images')
+    assert os.path.isdir(image_folder), 'Test image folder {} is not available'.format(image_folder)
+    inference_output_file = os.path.join(options.scratch_dir,'folder_inference_output.json')
+    if options.cli_working_dir is None:
+        cmd = 'python -m megadetector.detection.run_detector_batch'
+    else:
+        cmd = 'python megadetector/detection/run_detector_batch.py'
+    cmd += ' "{}" "{}" "{}" --recursive'.format(
+        options.default_model,image_folder,inference_output_file)
+    cmd += ' --output_relative_filenames --quiet --include_image_size'
+    cmd += ' --include_image_timestamp --include_exif_data'
+    print('Running: {}'.format(cmd))
+    cmd_results = execute_and_print(cmd)
+    
+    
+    ## Run again with checkpointing enabled, make sure the results are the same
+    
+    cmd += ' --checkpoint_frequency 5'
+    from megadetector.utils.path_utils import insert_before_extension
+    inference_output_file_checkpoint = insert_before_extension(inference_output_file,'_checkpoint')
+    assert inference_output_file_checkpoint != inference_output_file
+    cmd = cmd.replace(inference_output_file,inference_output_file_checkpoint)
+    print('Running: {}'.format(cmd))
+    cmd_results = execute_and_print(cmd)
+    
+    assert output_files_are_identical(fn1=inference_output_file, 
+                                      fn2=inference_output_file_checkpoint,verbose=True)
+    
+    
+    ## Postprocessing
+    
+    postprocessing_output_dir = os.path.join(options.scratch_dir,'postprocessing_output_cli')
+    
+    if options.cli_working_dir is None:
+        cmd = 'python -m megadetector.postprocessing.postprocess_batch_results'
+    else:
+        cmd = 'python megadetector/postprocessing/postprocess_batch_results.py'
+    cmd += ' "{}" "{}"'.format(
+        inference_output_file,postprocessing_output_dir)
+    cmd += ' --image_base_dir "{}"'.format(image_folder)
+    print('Running: {}'.format(cmd))
+    cmd_results = execute_and_print(cmd)
+                
+    
+    ## RDE
+    
+    rde_output_dir = os.path.join(options.scratch_dir,'rde_output_cli')
+    
+    if options.cli_working_dir is None:
+        cmd = 'python -m megadetector.postprocessing.repeat_detection_elimination.find_repeat_detections'
+    else:
+        cmd = 'python  megadetector/postprocessing/repeat_detection_elimination/find_repeat_detections.py'
+    cmd += ' "{}"'.format(inference_output_file)
+    cmd += ' --imageBase "{}"'.format(image_folder)
+    cmd += ' --outputBase "{}"'.format(rde_output_dir)
+    cmd += ' --occurrenceThreshold 1' # Use an absurd number here to make sure we get some suspicious detections
+    print('Running: {}'.format(cmd))
+    cmd_results = execute_and_print(cmd)    
+    
+    # Find the latest filtering folder
+    filtering_output_dir = os.listdir(rde_output_dir)
+    filtering_output_dir = [fn for fn in filtering_output_dir if fn.startswith('filtering_')]
+    filtering_output_dir = [os.path.join(rde_output_dir,fn) for fn in filtering_output_dir]
+    filtering_output_dir = [fn for fn in filtering_output_dir if os.path.isdir(fn)]
+    filtering_output_dir = sorted(filtering_output_dir)[-1]
+    
+    print('Using RDE filtering folder {}'.format(filtering_output_dir))
+    
+    filtered_output_file = inference_output_file.replace('.json','_filtered.json')
+    
+    if options.cli_working_dir is None:
+        cmd = 'python -m megadetector.postprocessing.repeat_detection_elimination.remove_repeat_detections'
+    else:
+        cmd = 'python  megadetector/postprocessing/repeat_detection_elimination/remove_repeat_detections.py'
+    cmd += ' "{}" "{}" "{}"'.format(inference_output_file,filtered_output_file,filtering_output_dir)
+    print('Running: {}'.format(cmd))
+    cmd_results = execute_and_print(cmd)
+    
+    assert os.path.isfile(filtered_output_file), \
+        'Could not find RDE output file {}'.format(filtered_output_file)
+    
+    
+    ## Run inference on a folder (tiled)
+    
+    image_folder = os.path.join(options.scratch_dir,'md-test-images')
+    tiling_folder = os.path.join(options.scratch_dir,'tiling-folder')
+    inference_output_file_tiled = os.path.join(options.scratch_dir,'folder_inference_output_tiled.json')
+    if options.cli_working_dir is None:
+        cmd = 'python -m megadetector.detection.run_tiled_inference'
+    else:
+        cmd = 'python megadetector/detection/run_tiled_inference.py'
+    cmd += ' "{}" "{}" "{}" "{}"'.format(
+        options.default_model,image_folder,tiling_folder,inference_output_file_tiled)
+    cmd += ' --overwrite_handling overwrite'
+    print('Running: {}'.format(cmd))
+    cmd_results = execute_and_print(cmd)
+    
+    with open(inference_output_file_tiled,'r') as f:
+        results_from_file = json.load(f) # noqa
+        
+    
+    ## Run inference on a folder (augmented)
+    
+    if options.yolo_working_dir is None:
+        
+        print('Bypassing YOLOv5 val tests, no yolo folder supplied')
+        
+    else:
+    
+        image_folder = os.path.join(options.scratch_dir,'md-test-images')
+        yolo_results_folder = os.path.join(options.scratch_dir,'yolo-output-folder')
+        yolo_symlink_folder = os.path.join(options.scratch_dir,'yolo-symlink_folder')
+        inference_output_file_yolo_val = os.path.join(options.scratch_dir,'folder_inference_output_yolo_val.json')
+        if options.cli_working_dir is None:
+            cmd = 'python -m megadetector.detection.run_inference_with_yolov5_val'
+        else:
+            cmd = 'python megadetector/detection/run_inference_with_yolov5_val.py'
+        cmd += ' "{}" "{}" "{}"'.format(
+            options.default_model,image_folder,inference_output_file_yolo_val)
+        cmd += ' --yolo_working_folder "{}"'.format(options.yolo_working_dir)
+        cmd += ' --yolo_results_folder "{}"'.format(yolo_results_folder)
+        cmd += ' --symlink_folder "{}"'.format(yolo_symlink_folder)
+        cmd += ' --augment_enabled 1'
+        # cmd += ' --no_use_symlinks'
+        cmd += ' --overwrite_handling overwrite'
+        print('Running: {}'.format(cmd))
+        cmd_results = execute_and_print(cmd)
+        
+        # Run again with checkpointing, make sure the output are identical
+        cmd += ' --checkpoint_frequency 5'
+        inference_output_file_yolo_val_checkpoint = \
+            os.path.join(options.scratch_dir,'folder_inference_output_yolo_val_checkpoint.json')
+        assert inference_output_file_yolo_val_checkpoint != inference_output_file_yolo_val
+        cmd = cmd.replace(inference_output_file_yolo_val,inference_output_file_yolo_val_checkpoint)
+        cmd_results = execute_and_print(cmd)
+        
+        assert output_files_are_identical(fn1=inference_output_file_yolo_val,
+                                          fn2=inference_output_file_yolo_val_checkpoint)
+        
+    if not options.skip_video_tests:
+            
+        ## Video test
+        
+        video_inference_output_file = os.path.join(options.scratch_dir,'video_inference_output.json')
+        output_video_file = os.path.join(options.scratch_dir,'video_scratch/cli_rendered_video.mp4')
+        frame_folder = os.path.join(options.scratch_dir,'video_scratch/frame_folder_cli')
+        frame_rendering_folder = os.path.join(options.scratch_dir,'video_scratch/rendered_frame_folder_cli')        
+        
+        video_fn = os.path.join(options.scratch_dir,options.test_videos[-1])        
+        assert os.path.isfile(video_fn), 'Could not find video file {}'.format(video_fn)
+        
+        output_dir = os.path.join(options.scratch_dir,'single_video_test_cli')
+        if options.cli_working_dir is None:
+            cmd = 'python -m megadetector.detection.process_video'
+        else:
+            cmd = 'python megadetector/detection/process_video.py'
+        cmd += ' "{}" "{}"'.format(options.default_model,video_fn)
+        cmd += ' --frame_folder "{}" --frame_rendering_folder "{}" --output_json_file "{}" --output_video_file "{}"'.format(
+            frame_folder,frame_rendering_folder,video_inference_output_file,output_video_file)
+        cmd += ' --render_output_video --fourcc {}'.format(options.video_fourcc)
+        cmd += ' --force_extracted_frame_folder_deletion --force_rendered_frame_folder_deletion --n_cores 5 --frame_sample 3'
+        cmd += ' --verbose'
+        print('Running: {}'.format(cmd))
+        cmd_results = execute_and_print(cmd)
+
+    # ...if we're not skipping video tests
+    
+    
+    ## Run inference on a folder (with MDV5B, so we can do a comparison)
+    
+    image_folder = os.path.join(options.scratch_dir,'md-test-images')
+    inference_output_file_alt = os.path.join(options.scratch_dir,'folder_inference_output_alt.json')
+    if options.cli_working_dir is None:
+        cmd = 'python -m megadetector.detection.run_detector_batch'
+    else:
+        cmd = 'python megadetector/detection/run_detector_batch.py'
+    cmd += ' "{}" "{}" "{}" --recursive'.format(
+        options.alt_model,image_folder,inference_output_file_alt)
+    cmd += ' --output_relative_filenames --quiet --include_image_size'
+    cmd += ' --include_image_timestamp --include_exif_data'
+    print('Running: {}'.format(cmd))
+    cmd_results = execute_and_print(cmd)
+    
+    with open(inference_output_file_alt,'r') as f:
+        results_from_file = json.load(f) # noqa
+    
+    
+    ## Compare the two files
+    
+    comparison_output_folder = os.path.join(options.scratch_dir,'results_comparison')
+    image_folder = os.path.join(options.scratch_dir,'md-test-images')
+    results_files_string = '"{}" "{}"'.format(
+        inference_output_file,inference_output_file_alt)
+    if options.cli_working_dir is None:
+        cmd = 'python -m megadetector.postprocessing.compare_batch_results'
+    else:
+        cmd = 'python megadetector/postprocessing/compare_batch_results.py'
+    cmd += ' "{}" "{}" {}'.format(comparison_output_folder,image_folder,results_files_string)
+    print('Running: {}'.format(cmd))
+    cmd_results = execute_and_print(cmd)
+    
+    assert cmd_results['status'] == 0, 'Error generating comparison HTML'
+    assert os.path.isfile(os.path.join(comparison_output_folder,'index.html')), \
+        'Failed to generate comparison HTML'
+    
+    print('\n*** Finished CLI tests ***\n')
+    
+# ...def run_cli_tests(...)
+
+
+#%% Main test wrapper
+
+def run_tests(options):
+    """
+    Runs Python-based and/or CLI-based package tests.
+    
+    Args:
+        options (MDTestOptions): see MDTestOptions for details
+    """
+    
+    # Prepare data folder
+    download_test_data(options)
+    
+    if options.disable_gpu:
+        os.environ['CUDA_VISIBLE_DEVICES'] = '-1'
+        
+    # Verify GPU
+    gpu_available = is_gpu_available()
+    
+    # If the GPU is required and isn't available, error
+    if options.cpu_execution_is_error and (not gpu_available):
+        raise ValueError('GPU not available, and cpu_execution_is_error is set')
+    
+    # If the GPU should be disabled, verify that it is
+    if options.disable_gpu:
+        assert (not gpu_available), 'CPU execution specified, but the GPU appears to be available'
+        
+    # Run python tests
+    if not options.skip_python_tests:
+        run_python_tests(options)
+    
+    # Run CLI tests
+    if not options.skip_cli_tests:
+        run_cli_tests(options)
+
+
+#%% Interactive driver
+
+if False:
+    
+    pass
+
+    #%%
+    
+    options = MDTestOptions()
+    
+    options.disable_gpu = False
+    options.cpu_execution_is_error = False
+    options.skip_video_tests = False
+    options.skip_python_tests = False
+    options.skip_cli_tests = False
+    options.scratch_dir = None
+    options.test_data_url = 'https://lila.science/public/md-test-package.zip'
+    options.force_data_download = False
+    options.force_data_unzip = False
+    options.warning_mode = True
+    options.max_coord_error = 0.001
+    options.max_conf_error = 0.005
+    options.cli_working_dir = r'c:\git\MegaDetector'
+    options.yolo_working_dir = r'c:\git\yolov5-md'
+
+
+    #%%
+    
+    run_tests(options)
+    
+    
+#%% Command-line driver
+
+def main():
+
+    options = MDTestOptions()
+    
+    parser = argparse.ArgumentParser(
+        description='MegaDetector test suite')
+    
+    parser.add_argument(
+        '--disable_gpu',
+        action='store_true',
+        help='Disable GPU operation')
+    
+    parser.add_argument(
+        '--cpu_execution_is_error',
+        action='store_true',
+        help='Fail if the GPU appears not to be available')
+    
+    parser.add_argument(
+        '--scratch_dir',
+        default=None,
+        type=str,
+        help='Directory for temporary storage (defaults to system temp dir)')
+    
+    parser.add_argument(
+        '--skip_video_tests',
+        action='store_true',
+        help='Skip tests related to video (which can be slow)')
+        
+    parser.add_argument(
+        '--skip_python_tests',
+        action='store_true',
+        help='Skip python tests')
+        
+    parser.add_argument(
+        '--skip_cli_tests',
+        action='store_true',
+        help='Skip CLI tests')
+        
+    parser.add_argument(
+        '--force_data_download',
+        action='store_true',
+        help='Force download of the test data file, even if it\'s already available')
+    
+    parser.add_argument(
+        '--force_data_unzip',
+        action='store_true',
+        help='Force extraction of all files in the test data file, even if they\'re already available')
+    
+    parser.add_argument(
+        '--warning_mode',
+        action='store_true',
+        help='Turns numeric/content errors into warnings')
+    
+    parser.add_argument(
+        '--max_conf_error',
+        type=float,
+        default=options.max_conf_error,
+        help='Maximum tolerable confidence value deviation from expected (default {})'.format(
+            options.max_conf_error))
+    
+    parser.add_argument(
+        '--max_coord_error',
+        type=float,
+        default=options.max_coord_error,
+        help='Maximum tolerable coordinate value deviation from expected (default {})'.format(
+            options.max_coord_error))
+
+    parser.add_argument(
+        '--cli_working_dir',
+        type=str,
+        default=None,
+        help='Working directory for CLI tests')
+    
+    parser.add_argument(
+        '--yolo_working_dir',
+        type=str,
+        default=None,
+        help='Working directory for yolo inference tests')
+
+    parser.add_argument(
+        '--cli_test_pythonpath',
+        type=str,
+        default=None,
+        help='PYTHONPATH to set for CLI tests; if None, inherits from the parent process'
+        )
+    
+    # token used for linting
+    #
+    # no_arguments_required
+        
+    args = parser.parse_args()
+    
+    _args_to_object(args,options)
+    
+    run_tests(options)
+    
+if __name__ == '__main__':    
+    main()
+
+
+#%% Sample invocations
+
+"""
+# Windows
+set PYTHONPATH=c:\git\MegaDetector;c:\git\yolov5-md
+python md_tests.py --cli_working_dir "c:\git\MegaDetector" --yolo_working_dir "c:\git\yolov5-md" --cli_test_pythonpath "c:\git\MegaDetector;c:\git\yolov5-md"
+
+# Linux
+export PYTHONPATH=/mnt/c/git/MegaDetector:/mnt/c/git/yolov5-md
+python md_tests.py --cli_working_dir "/mnt/c/git/MegaDetector" --yolo_working_dir "/mnt/c/git/yolov5-md" --cli_test_pythonpath "/mnt/c/git/MegaDetector:/mnt/c/git/yolov5-md"
+
+python -c "import md_tests; print(md_tests.get_expected_results_filename(True))"
+"""
+